Project: Ocean's dark energy: Global inventory of chemoautotrophs in the aphotic realm

From NSF award abstract:
The dark ocean, defined as the water column below the photic, contains one of the largest microbial biomes on earth, composed of active and metabolically diverse microorganisms. These biota impact local processes and the global carbon cycling, e.g. by conducting a large fraction of marine organic matter remineralization. An increasing body of evidence suggests that chemoautotrophy in the dark ocean may also be significant, with potentially major implications to the dark ocean's microbial ecology and biogeochemistry. However, it remains largely unanswered what energy sources and metabolic pathways are used to support this microbial-driven dark carbon fixation and which microbial taxonomic groups possess chemoautotrophic metabolic pathways in the dark ocean.

The overall goal of this project is to obtain a comprehensive, global inventory of chemoautotrophs in the dark ocean through large-scale microbial single cell genomics, supplemented with metagenomic and metatranscriptomic sequencing. The investigators will address the following general hypotheses:

1. Multiple prokaryote taxonomic groups found in the dark ocean contain chemoautotrophic metabolic pathways.

2. Both known and previously unrecognized chemoautotrophy pathways are present in dark ocean's prokaryotes.

3. Dark ocean chemoautotrophs are broadly distributed around the globe, with biogeographic patterns determined by the isopycnal movement of water masses, water mass age, and the downward flux of organic matter.

4. Diverse chemoautotrophy pathways are expressed in the dark ocean.

During the course of the project, single amplified genomes (SAGs) will be generated from all major intermediate and deep water masses around the globe, representing all major taxonomic groups of bacteria and archaea that are known to be present in the dark ocean. These SAGs will be analyzed for specific chemoautotrophy-indicative genes. Whole genome sequencing will be performed on a subset of SAGs, enabling detailed annotation of chemoautotrophy pathways. Metagenomic and metatranscriptomic fragment recruitment will be used to determine global patterns of chemoautotroph distribution and chemoautotrophy pathway expression. This ambitious project is made possible by the recent development of techniques and facilities for high-throughput genomic DNA recovery from individual cells at Bigelow Laboratory, genomic sequencing support provided by the U.S. Department of Energy Joint Genome Institute, and the establishment of a broad network of collaborations among many leading dark ocean microbiologists.

The project will generate a large quantity of unique reference materials, laying a solid foundation for future studies of dark ocean microorganisms, including 207 microbial genomes, representing all major taxonomic groups of bacteria and archaea from the dark ocean, multiple metagenomes, metatranscriptomes and pyrotag data sets, as well as genomic DNA from ~2,000 individual cells from diverse prokaryote taxonomic groups, water masses and geographic locations. The work will improve our understanding of the global carbon cycle, with direct relevance to climate change studies.

Publications produced as a result of this research:
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas, R. 2013. Prevalent genome streamlining and latitudinal divergence of marine planktonic bacteria in the surface ocean. PNAS, v.TBD, p. TBD, published online June 25, 2013. doi: 10.1073/pnas.1304246110